Substitute James Walker scored in injury time for Southend to deny Kevin Nugent a first victory in caretaker charge of Leyton Orient.
Orient took an 11th-minute lead when Adam Boyd fired in his ninth goal of the season after neat build-up play.
Southend's Alex Revell injured himself as he blasted over in the second half and was stretchered off, resulting in six minutes of injury time.
Walker took advantage, firing a superb right-foot shot into the top corner.
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Goals: Boyd 11.
Southend: Mildenhall, Sankofa, Francis, Barrett, Herd, Betsy, Grant (Walker 63), Christophe, Moussa, Revell (O'Keefe 84), Freedman (Barnard 21). Subs Not Used: Joyce, Scannell.
Booked: Grant, Christophe, Barrett.
Goals: Walker 90.
Att: 3,835
Ref: Oliver Langford (W Midlands).
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